Emergent survival and extinction of species within gut bacterial communities
van den Berg, N. I.; Tramontano, M.; Guan, R.; Andrejev, S.; Blasche, S.; Kim, Y.; Klunemann, M.; Gontao Brochado, A. R.; Kalmar, L.; Telzerow, A.; Bork, P.; Sevin, D.; Typas, A.; Patil, K. R.
Show abstract
Synthetic communities can help uncover metabolic forces shaping microbial ecosystems. Yet, in case of the gut microbiota, culturing in undefined media has prevented detection of metabolic dependencies. Here we show, using chemically defined media, how species survival is jointly determined by supplied resources and community metabolism. We used 63 representative gut bacterial strains and varied inoculum compositions to assemble stable communities in 14 defined media. Over 95% of the species showed markedly improved or diminished performance relative to monoculture in at least one condition, including 153 cases (21%) of emergent survival, i.e., species incapable of surviving on their own but thriving in a community, and 252 (35%) community-driven extinctions. Through single species additions and exclusions, metabolomic analysis, and ecological modelling, we demonstrate how inter-species dependencies - especially in poor media - are mediated by biotic nutrient supply. Our results highlight communal metabolic dividend as a key biotic force promoting emergent survival and diversity.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes. 96%
- Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes 96%
- Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales 96%
Similar papers in this journal
Similar papers in this journal
- A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors 96%
- Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome 95%
- Pairing Metagenomics and Metaproteomics to Characterize Ecological Niches and Metabolic Essentiality of gut microbiomes 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.